He's saying considerably more than that. The Constitution already explicitly prohibits the federal government from taxing one state to favor another. Madison's saying that the commerce clause, as it applies to interstate commerce, was not designed to be used "for the positive purposes of the general government" - exactly the opposite of what you said at #106.
In this letter, Madison is defining the original intent of the commerce clause and comparing it to the way he proposed that it be used in his previous letter where he suggested using the commerce clause against foreign imports for the positive purposes of the country.
The commerce clause was to be used to prevent or correct injustice among the States themselves. Even modern day interpretations of the commerce clause honor this original intent.